I usually build out three separate recipes in beer smith, first for the whole mash, batch size sum of first and second runnings beers, grist, hops etc. sum of whole batch (although this recipe is mostly for gravity and color calculations). Then I build out one recipe for the big beer and calc the hopping schedule for that and one for the small beer and use that to calc hopping for that. I don't re-use the hops though.
I have heard of people reusing dry hops later as a bittering charge but that's not really the same thing.